rs587776660

Variant names:

• chr19-1221993-ATCCGGCAGC-A
• rs587776660
• NM_000455.5:c.908_916delTCCGGCAGC

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PM4 PP3 PP5

The NM_000455.5(STK11):​c.908_916delTCCGGCAGC​(p.Ile303_His306delinsAsn) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 34)
• Consequence: STK11 NM_000455.5 disruptive_inframe_deletion
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 7.57

Genes affected

STK11 (HGNC:11389): (serine/threonine kinase 11) The protein encoded by this gene is a serine/threonine kinase that regulates cell polarity and energy metabolism and functions as a tumor suppressor. Mutations in this gene have been associated with the autosomal dominant Peutz-Jeghers syndrome, as well as with skin, pancreatic, and testicular cancers. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a domain Protein kinase (size 260) in uniprot entity STK11_HUMAN there are 19 pathogenic changes around while only 5 benign (79%) in NM_000455.5
• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000455.5.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 19-1221993-ATCCGGCAGC-A is Pathogenic according to our data. Variant chr19-1221993-ATCCGGCAGC-A is described in ClinVar as [Pathogenic]. Clinvar id is 7446.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK11	NM_000455.5	c.908_916delTCCGGCAGC	p.Ile303_His306delinsAsn	disruptive_inframe_deletion	Exon 7 of 10	ENST00000326873.12	NP_000446.1
STK11	NM_001407255.1	c.908_916delTCCGGCAGC	p.Ile303_His306delinsAsn	disruptive_inframe_deletion	Exon 7 of 9		NP_001394184.1
STK11	NR_176325.1	n.2175_2183delTCCGGCAGC		non_coding_transcript_exon_variant	Exon 8 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK11	ENST00000326873.12	c.908_916delTCCGGCAGC	p.Ile303_His306delinsAsn	disruptive_inframe_deletion	Exon 7 of 10	1	NM_000455.5	ENSP00000324856.6
STK11	ENST00000652231.1	c.908_916delTCCGGCAGC	p.Ile303_His306delinsAsn	disruptive_inframe_deletion	Exon 7 of 9			ENSP00000498804.1
STK11	ENST00000585748.3	c.536_544delTCCGGCAGC	p.Ile179_His182delinsAsn	disruptive_inframe_deletion	Exon 9 of 12	3		ENSP00000477641.2

Frequencies

GnomAD3 genomes Cov.: 34

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 34

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Peutz-Jeghers syndrome Pathogenic:1

Jan 08, 1998

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587776660; hg19: chr19-1221992;